Plot against z-coordinates

[askusay]

Hi CHAP team,

I have 2 CHAP profiles for two aligned ion channels.

The channels are different in height and therefore have different centres of mass but their channels are aligned. when I plot their profiles they are not aligned, presumably because of the difference in them COMs.

I typically plot the radius against data["pathwayProfile"]["s"]. Would it be possible to plot against the z-coordinate? All simulation frames are aligned

Thanks

[DSeiferth]

Unfortunately, there is no option to change the pathway coordinate from COM to z-coordinate.
In future releases of CHAP, we plan to add this feature.

Regarding your plots:
You could find the z-coordinate of the COM of the structures (for example with MDAnalysis) and shift the data["pathwayProfile"]["s"] array by adding constants such that the radius profiles are aligned.